combineKEGGnodes: Special treatment of nodes or edges for KEGG pathway rendering

Description

combineKEGGnodes combines nodes into a group in a KEGG pathway graph. reaction2edge converts reactions into edges in KEGG pathway graph.

Usage

combineKEGGnodes(nodes, graph, combo.node)
reaction2edge(path, gR)

Arguments

nodes

character, names of the names to be combined.

graph, gR

a object of "graphNEL" class, the graph parsed and converted from KEGG pathway.

path

a object of "KEGGPathway" class, the parsed KEGG pathway.

combo.node

character, the name of result combined node.

Value

The results returned by combineKEGGnodes is a combined graph of "graphNEL" class. The results returned by reaction2edge is a list of 3 elements: gR, the converted graph ("graphNEL"); edata.new, the new edge data ("KEGGEdge"); ndata.new, the new node data ("KEGGNode").

Details

combineKEGGnodes not only combines nodes in the graph object, but also corresponding node data in the KEGG pathway object. This function is needed for KEGG-defined group nodes and parsed enzyme groups involved in the same reaction. reaction2edge converts a reaction into 2 consecutive edges between substrate and enzyme and enzyme and product. This function is needed as to faithfully show the compound-enzyme nodes and their interactions in Graphviz-style view of KEGG pathway.

References